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This page was generated on 2017-08-16 13:44:28 -0400 (Wed, 16 Aug 2017).
| Package 1309/1410 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| STRINGdb 1.17.1 Damian Szklarczyk
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK |  | |||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | |||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK |
| Package: STRINGdb |
| Version: 1.17.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings STRINGdb_1.17.1.tar.gz |
| StartedAt: 2017-08-16 08:59:40 -0400 (Wed, 16 Aug 2017) |
| EndedAt: 2017-08-16 09:00:21 -0400 (Wed, 16 Aug 2017) |
| EllapsedTime: 41.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: STRINGdb.Rcheck |
| Warnings: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings STRINGdb_1.17.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/STRINGdb.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘STRINGdb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘STRINGdb’ version ‘1.17.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘STRINGdb’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 8.5Mb
sub-directories of 1Mb or more:
doc 7.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
coeffOfvar: no visible global function definition for ‘sd’
downloadAbsentFile: no visible global function definition for ‘tail’
downloadAbsentFile: no visible global function definition for
‘download.file’
downloadAbsentFileSTRING: no visible global function definition for
‘read.table’
downloadAbsentFileSTRING: no visible global function definition for
‘tail’
downloadAbsentFileSTRING: no visible global function definition for
‘download.file’
get_STRING_species: no visible global function definition for
‘read.table’
plot_ppi_enrichment_graph: no visible global function definition for
‘pdf’
plot_ppi_enrichment_graph: no visible global function definition for
‘jpeg’
plot_ppi_enrichment_graph: no visible global function definition for
‘plot’
plot_ppi_enrichment_graph: no visible global function definition for
‘abline’
plot_ppi_enrichment_graph: no visible global function definition for
‘dev.off’
ppi_enrichment: no visible global function definition for ‘ppois’
ppi_enrichment_full: no visible global function definition for
‘txtProgressBar’
ppi_enrichment_full: no visible global function definition for
‘setTxtProgressBar’
ppi_enrichment_full: no visible global function definition for ‘ppois’
Undefined global functions or variables:
abline dev.off download.file jpeg pdf plot ppois read.table sd
setTxtProgressBar tail txtProgressBar
Consider adding
importFrom("grDevices", "dev.off", "jpeg", "pdf")
importFrom("graphics", "abline", "plot")
importFrom("stats", "ppois", "sd")
importFrom("utils", "download.file", "read.table", "setTxtProgressBar",
"tail", "txtProgressBar")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
Test files with failing tests
test_get_homologs.R
test_get_homologs
test_get_homologs_besthits.R
test_get_homologs_besthits
test_get_pubmed_interaction.R
test_get_pubmed_interaction
Error in BiocGenerics:::testPackage("STRINGdb") :
unit tests failed for package STRINGdb
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/STRINGdb.Rcheck/00check.log’
for details.
runTests.Rout.fail:
R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("STRINGdb")
Timing stopped at: 0.039 0.002 0.344
Error in open.connection(file, "rt") :
cannot open the connection to 'http://string.uzh.ch/permanent/string/r_lib_valid_versions'
In addition: Warning message:
In open.connection(file, "rt") :
URL 'http://string.uzh.ch/permanent/string/r_lib_valid_versions': status was 'Couldn't connect to server'
Timing stopped at: 0.032 0 0.342
Error in open.connection(file, "rt") :
cannot open the connection to 'http://string.uzh.ch/permanent/string/r_lib_valid_versions'
In addition: Warning messages:
1: closing unused connection 3 (http://string.uzh.ch/permanent/string/r_lib_valid_versions)
2: In open.connection(file, "rt") :
URL 'http://string.uzh.ch/permanent/string/r_lib_valid_versions': status was 'Couldn't connect to server'
Timing stopped at: 0.002 0 0.327
Error in open.connection(file, "rt") :
cannot open the connection to 'http://string.uzh.ch/permanent/string/r_lib_valid_versions'
In addition: Warning messages:
1: In .Internal(gc(verbose, reset)) :
closing unused connection 3 (http://string.uzh.ch/permanent/string/r_lib_valid_versions)
2: In open.connection(file, "rt") :
URL 'http://string.uzh.ch/permanent/string/r_lib_valid_versions': status was 'Couldn't connect to server'
RUNIT TEST PROTOCOL -- Wed Aug 16 09:00:17 2017
***********************************************
Number of test functions: 3
Number of errors: 3
Number of failures: 0
1 Test Suite :
STRINGdb RUnit Tests - 3 test functions, 3 errors, 0 failures
ERROR in test_get_homologs: Error in open.connection(file, "rt") :
cannot open the connection to 'http://string.uzh.ch/permanent/string/r_lib_valid_versions'
ERROR in test_get_homologs_besthits: Error in open.connection(file, "rt") :
cannot open the connection to 'http://string.uzh.ch/permanent/string/r_lib_valid_versions'
ERROR in test_get_pubmed_interaction: Error in open.connection(file, "rt") :
cannot open the connection to 'http://string.uzh.ch/permanent/string/r_lib_valid_versions'
Test files with failing tests
test_get_homologs.R
test_get_homologs
test_get_homologs_besthits.R
test_get_homologs_besthits
test_get_pubmed_interaction.R
test_get_pubmed_interaction
Error in BiocGenerics:::testPackage("STRINGdb") :
unit tests failed for package STRINGdb
Execution halted
STRINGdb.Rcheck/00install.out:
* installing *source* package ‘STRINGdb’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (STRINGdb)
STRINGdb.Rcheck/STRINGdb-Ex.timings:
| name | user | system | elapsed | |
| STRINGdb-class | 0.002 | 0.000 | 0.002 | |